Property map collective variable as a usefultool for force field correction - analysis ...
Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the d...
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ftdatacite:10.5281/zenodo.4906267 2023-06-11T04:15:47+02:00 Property map collective variable as a usefultool for force field correction - analysis ... Trapl, Dalibor Krupicka, Martin Visnovsky, Vladimir Hozzova, Jana Olha, Jaroslav Krenek, Ales Spiwok, Vojtech 2021 https://dx.doi.org/10.5281/zenodo.4906267 https://zenodo.org/record/4906267 unknown Zenodo https://zenodo.org/communities/elixir-cz https://dx.doi.org/10.5281/zenodo.4906268 https://zenodo.org/communities/elixir-cz Open Access Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 info:eu-repo/semantics/openAccess molecular dynamics simulation metadynamics molecular mechanics article-journal JournalArticle ScholarlyArticle 2021 ftdatacite https://doi.org/10.5281/zenodo.490626710.5281/zenodo.4906268 2023-05-02T10:00:59Z Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT). Simulations were carried out in Gromacs 2016.4. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory. Here we present input and output files for analysis by Plumed, R with Rmarkdown and Metadynminer. The analysis can be initialized ... Article in Journal/Newspaper Orca DataCite Metadata Store (German National Library of Science and Technology) Lambda ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
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Open Polar |
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DataCite Metadata Store (German National Library of Science and Technology) |
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ftdatacite |
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unknown |
topic |
molecular dynamics simulation metadynamics molecular mechanics |
spellingShingle |
molecular dynamics simulation metadynamics molecular mechanics Trapl, Dalibor Krupicka, Martin Visnovsky, Vladimir Hozzova, Jana Olha, Jaroslav Krenek, Ales Spiwok, Vojtech Property map collective variable as a usefultool for force field correction - analysis ... |
topic_facet |
molecular dynamics simulation metadynamics molecular mechanics |
description |
Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT). Simulations were carried out in Gromacs 2016.4. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory. Here we present input and output files for analysis by Plumed, R with Rmarkdown and Metadynminer. The analysis can be initialized ... |
format |
Article in Journal/Newspaper |
author |
Trapl, Dalibor Krupicka, Martin Visnovsky, Vladimir Hozzova, Jana Olha, Jaroslav Krenek, Ales Spiwok, Vojtech |
author_facet |
Trapl, Dalibor Krupicka, Martin Visnovsky, Vladimir Hozzova, Jana Olha, Jaroslav Krenek, Ales Spiwok, Vojtech |
author_sort |
Trapl, Dalibor |
title |
Property map collective variable as a usefultool for force field correction - analysis ... |
title_short |
Property map collective variable as a usefultool for force field correction - analysis ... |
title_full |
Property map collective variable as a usefultool for force field correction - analysis ... |
title_fullStr |
Property map collective variable as a usefultool for force field correction - analysis ... |
title_full_unstemmed |
Property map collective variable as a usefultool for force field correction - analysis ... |
title_sort |
property map collective variable as a usefultool for force field correction - analysis ... |
publisher |
Zenodo |
publishDate |
2021 |
url |
https://dx.doi.org/10.5281/zenodo.4906267 https://zenodo.org/record/4906267 |
long_lat |
ENVELOPE(-62.983,-62.983,-64.300,-64.300) |
geographic |
Lambda |
geographic_facet |
Lambda |
genre |
Orca |
genre_facet |
Orca |
op_relation |
https://zenodo.org/communities/elixir-cz https://dx.doi.org/10.5281/zenodo.4906268 https://zenodo.org/communities/elixir-cz |
op_rights |
Open Access Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.5281/zenodo.490626710.5281/zenodo.4906268 |
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1768372904829911040 |